[gmx-users] Position Restraints of one of the moleculetpye

Justin A. Lemkul jalemkul at vt.edu
Mon May 28 18:25:11 CEST 2012

On 5/28/12 10:48 AM, Steven Neumann wrote:
> Dear Gmx Users,
> I am fighting with the position restraints. My system cosnsists of 6 ligands -
> all of them have the same topology - ligand.itp. I want to:
> 1. Run NPT restraining all of ligands (easy: -DPOSRES_L, ifdef POSRE_L, posre
> ligand1.itp
> 2. Restrain 5 of them and pull one of them away.
> Here I came across some difficulties.
> I used genrestr -f 6ligands.gro -n index.ndx -o posre1.itp
> and by index files I create an index of the ligands I wan to restrain. Each my
> ligands has 46 atoms. When I process to grompp:
> Atom index (256) in position_restraints out of bounds (1-46).
> This probably means that you have inserted topology section "position_restraints
> Shall I rename Ligands as different residue names? If my posre includes 1-46
> atom all ligands are restraints? How to restrain just 5 out of 6 of them?

Position restraints are applied on a per-moleculetype basis.  If you have six 
copies of a ligand, the only way to do this is to define the sixth as a special 
[moleculetype] (even if it contains identical information) with a different 
name, such that it can be restrained in the absence of restraints on the others. 
  See the logic here:




Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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